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1.	Munthe, Christian, 1962 (författare) Precaution and Ethics: Handling risks, uncertainties and knowledge gaps in the regulation of new biotechnologies 2017 Bok (övrigt vetenskapligt/konstnärligt)abstract This volume outlines and analyses ethical issues actualized by applying a precautionary approach to the regulation of new biotechnologies. It presents a novel way of categorizing and comparing biotechnologies from a precautionary standpoint. Based on this, it addresses underlying philosophical problems regarding the ethical assessment of decision-making under uncertainty and ignorance, and discusses how risks and possible benefits of such technologies should be balanced from an ethical standpoint. It argues on conceptual and ethical grounds for a technology neutral regulation as well as for a regulation that not only checks new technologies but also requires old, inferior ones to be phased out. It demonstrates how difficult ethical issues regarding the extent and ambition of precautionary policies need to be handled by such a regulation, and presents an overarching framework for doing so.
2.	Sandin, Per, et al. (författare) Technology neutrality and regulation of agricultural biotechnology 2018 Ingår i: Professionals in food chains: ethics, rules and responsibility. EurSafe 2018, Vienna, Austria 13 – 16 June 2018 / edited by: Svenja Springer, Herwig Grimm. - Wageningen, Netherlands : Wageningen Academic Publishers. - 9789086863211 Konferensbidrag (refereegranskat)abstract Agricultural biotechnology, in particular genetically modified organisms (GMOs), is subject to regulation in many areas of the world, not least in the European Union (EU). A number of authors have argued that those regulatory processes are unfair, costly, and slow and that regulation therefore should move in the direction of increased ‘technology neutrality’. The issue is becoming more pressing, especially since new biotechnologies such as CRISPR increasingly blur the regulatory distinction between GMOs and non-GMOs. This paper offers a definition of technology neutrality, uses the EU GMO regulation as a starting point for exploring technology neutrality, and presents distinctions between variants of the call for technology neutral GMO regulation in the EU.
3.	Schrader, J., et al. (författare) Cambial meristem dormancy in trees involves extensive remodelling of the transcriptome 2004 Ingår i: The Plant Journal. - Malden : Wiley-Blackwell. - 0960-7412 .- 1365-313X. ; 40:2, s. 173-187 Tidskriftsartikel (refereegranskat)abstract The establishment of the dormant state in meristems involves considerable physiological and metabolic alterations necessary for surviving unfavourable growth conditions. However, a global molecular analysis of dormancy in meristems has been hampered by the difficulty in isolating meristem cells. We used cryosectioning to isolate purified cambial meristem cells from the woody plant Populus tremula during active growth and dormancy. These samples were used to generate meristem-specific cDNA libraries and for cDNA microarray experiments to define the global transcriptional changes underlying cambial dormancy. The results indicate a significant reduction in the complexity of the cambial transcriptome in the dormant state. Although cell division is terminated in the dormant cambium, the cell cycle machinery appears to be maintained in a skeletal state as suggested by the continued presence of transcripts for several cell cycle regulators. The downregulation of PttPIN1 and PttPIN2 transcripts explains the reduced basipetal polar auxin transport during dormancy. The induction of a member of the SINA family of ubiquitin ligases implicated in auxin signalling indicates a potential mechanism for modulation of auxin sensitivity during cambial dormancy. The metabolic alterations during dormancy are mirrored in the induction of genes involved in starch breakdown and the glyoxysomal cycle. Interestingly, the induction of RGA1 like gene suggests modification of gibberellin signalling in cambial dormancy. The induction of genes such as poplar orthologues of FIE and HAP2 indicates a potential role for these global regulators of transcription in orchestrating extensive changes in gene expression during dormancy.
4.	Sweetlove, Lee J., et al. (författare) Engineering central metabolism – a grand challenge for plant biologists 2017 Ingår i: Plant Journal. - : Wiley. - 0960-7412 .- 1365-313X. ; 90:4, s. 749-763 Tidskriftsartikel (refereegranskat)abstract The goal of increasing crop productivity and nutrient-use efficiency is being addressed by a number of ambitious research projects seeking to re-engineer photosynthetic biochemistry. Many of these projects will require the engineering of substantial changes in fluxes of central metabolism. However, as has been amply demonstrated in simpler systems such as microbes, central metabolism is extremely difficult to rationally engineer. This is because of multiple layers of regulation that operate to maintain metabolic steady state and because of the highly connected nature of central metabolism. In this review we discuss new approaches for metabolic engineering that have the potential to address these problems and dramatically improve the success with which we can rationally engineer central metabolism in plants. In particular, we advocate the adoption of an iterative ‘design-build-test-learn’ cycle using fast-to-transform model plants as test beds. This approach can be realised by coupling new molecular tools to incorporate multiple transgenes in nuclear and plastid genomes with computational modelling to design the engineering strategy and to understand the metabolic phenotype of the engineered organism. We also envisage that mutagenesis could be used to fine-tune the balance between the endogenous metabolic network and the introduced enzymes. Finally, we emphasise the importance of considering the plant as a whole system and not isolated organs: the greatest increase in crop productivity will be achieved if both source and sink metabolism are engineered.
5.	Abebe, Admas Alemu, et al. (författare) Genomic selection in plant breeding: key factors shaping two decades of progress 2024 Ingår i: Molecular Plant. - 1674-2052 .- 1752-9867. ; 17, s. 552-578 Forskningsöversikt (refereegranskat)abstract Genomic selection, the application of genomic prediction (GP) models to select candidate individuals, has significantly advanced in the past two decades, effectively accelerating genetic gains in plant breeding. This article provides a holistic overview of key factors that have influenced GP in plant breeding during this period. We delved into the pivotal roles of training population size and genetic diversity, and their relationship with the breeding population, in determining GP accuracy. Special emphasis was placed on optimizing training population size. We explored its benefits and the associated diminishing returns beyond an optimum size. This was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization algorithms. The density and distribution of single-nucleotide polymorphisms, level of linkage disequilibrium, genetic complexity, trait heritability, statistical machine-learning methods, and non-additive effects are the other vital factors. Using wheat, maize, and potato as examples, we summarize the effect of these factors on the accuracy of GP for various traits. The search for high accuracy in GP—theoretically reaching one when using the Pearson’s correlation as a metric—is an active research area as yet far from optimal for various traits. We hypothesize that with ultra-high sizes of genotypic and phenotypic datasets, effective training population optimization methods and support from other omics approaches (transcriptomics, metabolomics and proteomics) coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy, making genomic selection an effective tool in plant breeding.
6.	Abreha, Kibrom Berhe, et al. (författare) Understanding the Sorghum–Colletotrichum sublineola interactions for enhanced host resistance 2021 Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 12 Forskningsöversikt (refereegranskat)abstract Improving sorghum resistance is a sustainable method to reduce yield losses due to anthracnose, a devastating disease caused by Colletotrichum sublineola. Elucidating the molecular mechanisms of sorghum–C. sublineola interactions would help identify biomarkers for rapid and efficient identification of novel sources for host-plant resistance improvement, understanding the pathogen virulence, and facilitating resistance breeding. Despite concerted efforts to identify resistance sources, the knowledge about sorghum–anthracnose interactions remains scanty. Hence, in this review, we presented an overview of the current knowledge on the mechanisms of sorghum-C. sublineola molecular interactions, sources of resistance for sorghum breeding, quantitative trait loci (QTL), and major (R-) resistance gene sequences as well as defense-related genes associated with anthracnose resistance. We summarized current knowledge about C. sublineola populations and its virulence. Illustration of the sorghum-C. sublineola interaction model based on the current understanding is also provided. We highlighted the importance of genomic resources of both organisms for integrated omics research to unravel the key molecular components underpinning compatible and incompatible sorghum–anthracnose interactions. Furthermore, sorghum-breeding strategy employing rapid sorghum germplasm screening, systems biology, and molecular tools is presented.
7.	Ahmadi Afzadi, Masoud (författare) Genetic variation in resistance to fungal storage diseases in apple : inoculation-based screening, transcriptomics and biochemistry 2015 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Apple is one of the economically and culturally most important fruit crops and has many health-related benefits. Apple production is, however, sensitive to several fungal diseases including blue mold, caused by Penicillium expansum. Problems are more pronounced in organic production or in countries where postharvest application of fungicides is prohibited. To limit or overcome this problem, many studies have been focused on investigations of the mechanism of resistance/tolerance. No major gene(s) have as yet been identified, but quantitatively inherited traits, some of which are related to fruit texture and content of chemical compounds, have been shown to affect the ability of cultivars to withstand storage diseases. In the present thesis, inter-cultivar variation in terms of resistance to fungal storage diseases was investigated at two locations, i.e. Balsgård in Sweden and Njøs in Norway. The association of harvest date, fruit firmness and softening with lesion decay was investigated on large sets of cultivars. The contribution of four fruit texture-related genes (Md-ACO1, Md-ACS1, Md-Exp7 and Md-PG1) in explaining the fruit texture characteristics was examined. Fruit content of chemical compounds with a potential impact on disease resistance was also investigated, and finally the regulation of apple genes upon fungal infection was studied in order to identify candidate genes responsible for disease resistance. Inoculation-based screening indicated large variation across the investigated cultivars in terms of blue mold and bitter rot susceptibility. Harvest date and softening rate of fruits during storage had a large impact on resistance to fungal diseases, thus cultivars with moderate to firm fruits that soften comparatively little during storage could withstand the fungal infection comparatively well. Softening rate is, in its turn, closely associated with harvest date whereas four fruit texture-related genes had lower predictive power than expected. Quantifying the chemical compounds in the fruit samples revealed that some of these compounds, especially flavonols and procyanidin B2, could contribute to resistance against blue mold, whereas contents of malic acids or total titratable acidity had considerably less impact. Differential expression of FLS, LDOX, and CHS genes involved in biosynthesis of flavonoids and PGIP, TT10, WAK1 and CTL1 genes related to cell wall structure indicate the importance of fruit characteristics and biochemical compounds in the resistance mechanism.
8.	Alexandersson, Erik, et al. (författare) Tro får inte ersätta vetenskap 2014 Ingår i: Svenska dagbladet. - 1101-2412. Tidskriftsartikel (populärvet., debatt m.m.)
9.	Andersson, Mariette (författare) Comparative Transcriptome Analysis of Three Oil Palm Fruit and Seed Tissues That Differ in Oil Content and Fatty Acid Composition 2013 Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 162, s. 1337-1358 Tidskriftsartikel (refereegranskat)abstract Oil palm (Elaeis guineensis) produces two oils of major economic importance, commonly referred to as palm oil and palm kernel oil, extracted from the mesocarp and the endosperm, respectively. While lauric acid predominates in endosperm oil, the major fatty acids (FAs) of mesocarp oil are palmitic and oleic acids. The oil palm embryo also stores oil, which contains a significant proportion of linoleic acid. In addition, the three tissues display high variation for oil content at maturity. To gain insight into the mechanisms that govern such differences in oil content and FA composition, tissue transcriptome and lipid composition were compared during development. The contribution of the cytosolic and plastidial glycolytic routes differed markedly between the mesocarp and seed tissues, but transcriptional patterns of genes involved in the conversion of sucrose to pyruvate were not related to variations for oil content. Accumulation of lauric acid relied on the dramatic up-regulation of a specialized acyl-acyl carrier protein thioesterase paralog and the concerted recruitment of specific isoforms of triacylglycerol assembly enzymes. Three paralogs of the WRINKLED1 (WRI1) transcription factor were identified, of which EgWRI1-1 and EgWRI1-2 were massively transcribed during oil deposition in the mesocarp and the endosperm, respectively. None of the three WRI1 paralogs were detected in the embryo. The transcription level of FA synthesis genes correlated with the amount of WRI1 transcripts and oil content. Changes in triacylglycerol content and FA composition of Nicotiana benthamiana leaves infiltrated with various combinations of WRI1 and FatB paralogs from oil palm validated functions inferred from transcriptome analysis.
10.	Andersson, Mariette, et al. (författare) Genome editing in potato via CRISPR-Cas9 ribonucleoprotein delivery 2018 Ingår i: Physiologia Plantarum. - : Wiley. - 0031-9317 .- 1399-3054. ; 164, s. 378-384 Tidskriftsartikel (refereegranskat)abstract Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein-9 (CRISPR-Cas9) can be used as an efficient tool for genome editing in potato (Solanum tuberosum). From both a scientific and a regulatory perspective, it is beneficial if integration of DNA in the potato genome is avoided. We have implemented a DNA-free genome editing method, using delivery of CRISPR-Cas9 ribonucleoproteins (RNPs) to potato protoplasts, by targeting the gene encoding a granule bound starch synthase (GBSS, EC 2.4.1.242). The RNP method was directly implemented using previously developed protoplast isolation, transfection and regeneration protocols without further adjustments. Cas9 protein was preassembled with RNA produced either synthetically or by in vitro transcription. RNP with synthetically produced RNA (cr-RNP) induced mutations, i.e. indels, at a frequency of up to 9%, with all mutated lines being transgene-free. A mutagenesis frequency of 25% of all regenerated shoots was found when using RNP with in vitro transcriptionally produced RNA (IVT-RNP). However, more than 80% of the shoots with confirmed mutations had unintended inserts in the cut site, which was in the same range as when using DNA delivery. The inserts originated both from DNA template remnants from the in vitro transcription, and from chromosomal potato DNA. In 2-3% of the regenerated shoots from the RNP-experiments, mutations were induced in all four alleles resulting in a complete knockout of the GBSS enzyme function.
11.	Andreasson, Erik, et al. (författare) Insights on cisgenic plants with durable disease resistance under the European Green Deal 2023 Ingår i: Trends in Biotechnology. - 0167-7799 .- 1879-3096. ; 41, s. 1027-1040 Forskningsöversikt (refereegranskat)abstract Significant shares of harvests are lost to pests and diseases, therefore, minimizing these losses could solve part of the supply constraints to feed the world. Cisgenesis is defined as the insertion of genetic material into a recipient organism from a donor that is sexually compatible. Here, we review (i) conventional plant breeding, (ii) cisgenesis, (iii) current pesticide-based disease management, (iv) potential economic implications of cultivating cisgenic crops with durable disease resistances, and (v) potential environmental implications of cultivating such crops; focusing mostly on potatoes, but also apples, with resistances to Phytophthora infestans and Venturia inaequalis, respectively. Adopting cisgenic varieties could provide benefits to farmers and to the environment through lower pesticide use, thus contributing to the European Green Deal target.
12.	Arif, Usman (författare) Effect of wounding and light exposure on sterol, glycoalkaloid, and calystegine levels in potato plants (Solanum tuberosum L. group Tuberosum) 2013 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Steroidal glycoalkaloids (SGA) are neurotoxic substances that are present in some members of the Solanaceae family, including crop species like potato (Solanum tuberosum L.) and tomato. The SGA level in the potato tuber is a genetic trait, but certain environmental factors such as wounding and light exposure can increase SGA levels several-fold, which may render tubers unsuitable for human consumption. There is little information about SGA biosynthesis. The sterol cholesterol is commonly regarded as a SGA precursor, but there is little evidence for this view. To increase our understanding of the SGA biosynthesis and its molecular regulation, a microarray screen was performed using tubers from two potato cultivars subjected to wound and light treatments. Along with an alteration of sterol and SGA levels, the treatments were associated with an up-regulation of a small set of genes in sterol and SGA metabolism, including a gene encoding for the sterol reductase DWF1. DWF1 genes were found in two differentially regulated subtypes; DWF1 and DWF1-like (DWF1-L). Alteration of DWF1 and DWF1-L expression in transgenic potato showed a role for these genes in sterol and SGA synthesis. Also up-regulated in the microarray study were three transaminase-like genes, and role of StTAM1 in SGA synthesis was investigated by overexpression in transgenic potato. This resulted in elevated SGA levels, indicating the presence of a transamination in SGA synthesis. The genetic variation and stress responsiveness in Swedish potato cultivars regarding SGA and calystegine alkaloids (CA) level was determined by subjecting tubers to wounding, light exposure and elevated temperature. Only light and wounding increased SGA levels, and variation in the response was observed among the cultivars. CA levels were not stress-regulated, indicating that SGA and CA synthesis are not interrelated. These results show that the SGA level in potato tubers are regulated by a concerted action of a small set of key genes acting at different steps in the sterol and SGA pathways. Results also demonstrate a genetic variation in stress responsiveness among Swedish potato cultivars, and have identified the most sensitive ones. Results could in the near future be used to improve post-harvest handling of potato cultivars.
13.	Brhanie Mesfin, Haftom, et al. (författare) Novel GBS-Based SNP Markers for Finger Millet and Their Use in Genetic Diversity Analyses 2022 Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 13 Tidskriftsartikel (refereegranskat)abstract Eleusine coracana (L.) Gaertn., commonly known as finger millet, is a multipurpose crop used for food and feed. Genomic tools are required for the characterization of crop gene pools and their genomics-led breeding. High-throughput sequencing-based characterization of finger millet germplasm representing diverse agro-ecologies was considered an effective method for determining its genetic diversity, thereby suggesting potential candidates for breeding. In this study, the genotyping-by-sequencing (GBS) method was used to simultaneously identify novel single nucleotide polymorphism (SNP) markers and genotype 288 finger millet accessions collected from Ethiopia and Zimbabwe. The accessions were characterized at individual and group levels using 5,226 bi-allelic SNPs, with a minimum allele frequency (MAF) of above 0.05, distributed across 2,500 scaffolds of the finger millet reference genome. The polymorphism information content (PIC) of the SNPs was 0.23 on average, and a quarter of them have PIC values over 0.32, making them highly informative. The grouping of the 288 accessions into seven populations based on geographic proximity and the potential for germplasm exchange revealed a narrow range of observed heterozygosity (Ho; 0.09-0.11) and expected heterozygosity (He) that ranged over twofold, from 0.11 to 0.26. Alleles unique to the different groups were also identified, which merit further investigation for their potential association with desirable traits. The analysis of molecular variance (AMOVA) revealed a highly significant genetic differentiation among groups of accessions classified based on the geographic region, country of origin, days to flowering, panicle type, and Al tolerance (p < 0.01). The high genetic differentiation between Ethiopian and Zimbabwean accessions was evident in the AMOVA, cluster, principal coordinate, and population structure analyses. The level of genetic diversity of finger millet accessions varies moderately among locations within Ethiopia, with accessions from the northern region having the lowest level. In the neighbor-joining cluster analysis, most of the improved cultivars included in this study were closely clustered, probably because they were developed using genetically less diverse germplasm and/or selected for similar traits, such as grain yield. The recombination of alleles via crossbreeding genetically distinct accessions from different regions of the two countries can potentially lead to the development of superior cultivars.
14.	Burra, Dharani (författare) Defence related molecular signalling in Potato : new perspectives from “- Omics” 2016 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Potato production is hampered by several pathogens and is subjected to intense chemical based disease control, use of which also has undesirable consequences. Resistance breeding programs have also shown limited success. Hence, there is a need to develop durable disease resistance. Omics-techniques enable new layers of knowledge regarding molecules and their interactions mediating defence, which can contribute to identification of durable resistance sources. A novel network-based approach was used to improve the existing annotation of gene probes on the genome based microarray. Approximately 8000 unannotated probes received a new annotation. This improved annotation was used to assess genome wide changes in transcripts and proteins in response to treatments with resistance inducers, β- amino butyric acid (BABA) and Phosphite based salt (Phi). Five thousand transcripts were significantly regulated 48 hours after 10mM BABA treatment while one was regulated with 1mM BABA. In coherence, 10 mM BABA but not 1 mM induced protection to the hemibiotroph Phytophthora infestans. No transcript was significantly regulated 48 hours after Phi treatment. Time course analysis revealed that Phi exerts a transient effect, as significant transcriptomic changes were observed only 3, 6 and 11 hours after treatment. In contrast, plants showed resistance to P. infestans even at 120 hours after Phi treatment. Phi and BABA dependent “Induced state” is not restricted to transcripts related to plant defence, as transcripts related to abiotic stress and primary metabolism were altered, while biotic stress and cell wall related proteins also increased in abundance. Furthermore, an in vitro based blackleg disease screening assay was developed to investigate Potato – Dickeya solani interactions. We show that salicylic (SA) and COI1 are necessary for defence in shoots and tubers to this necrotroph. We also screened a crossing population and identified “potential” D. solani susceptibility genes related to transcriptional regulation. We also show that while SA is necessary to restrict lesion development and pathogen growth in response to the necrotroph Alternaria solani, COI1 affects pathogen growth only. Transcriptomic analysis indicated that rapid defence response to A. solani involves biotic, abiotic and oxidative stress related transcripts regulated by SA and COI1. We identified a citrate binding protein, which is also induced by resistance inducers, as an SA-repressed susceptibility factor to A. solani. Finally, proteomics of PAMP triggered immunity revealed upregulation of oxidative stress proteins while proteins related to oxidative stress tolerance, GTP binding activity were specifically upregulated in effector triggered immunity interactions.
15.	Calleja-Rodriguez, Ainhoa, et al. (författare) Functional QTL Analysis for Adaptive Traits in a Three-Generation Scots Pine Pedigree 2018 Konferensbidrag (övrigt vetenskapligt/konstnärligt)
16.	Calleja-Rodriguez, Ainhoa (författare) Quantitative Genetics and Genomic Selection of Scots pine 2019 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract The final objective of tree improvement programs is to increase the frequency of favourable alleles in a population, for the traits of interest within the breeding programs. To achieve this, it is crucial to decompose the phenotypic variance accurately into its genetic and environmental components in order to obtain a precise estimation of genetic parameters and to increase genetic gains. The overall aim of this thesis was to increase the accuracy of genetic parameter estimation by incorporating new quantitative genetics models to the analysis of multiple traits in multiple trials of Scots pine, and to develop a genomic selection protocol to accelerate genetic gain. Factor analysis was incorporated to multivariate multi-environment analyses and it allowed to evaluate up to 19 traits simultaneously. As a result, precise patterns of genotype-by-environment interactions (G  E) were observed for tree vitality and height; moreover, it was possible to detect the main driver of the G  E: differences in temperature sum among sites. Traditional quantitative trait loci (QTL) analysis of phenotypic data was compared with the detection of QTL with estimated breeding values (EBV) for the first time in a three generation pedigree and, as outcome, it was noticed that if a QTL was associated to a EBV and to a phenotypic trait, the proportion of variance explained by the QTLEBV was higher than the QTL-phenotype. Additionally, several QTL were detected across several ages, which may make them suitable as candidates for early selection. Genomic selection (GS) could aid to reduce the breeding cycle by shortening the periods of progeny field testing, and consequently increasing genetic gains per year. Genomic predictions, including additive and non-additive effects through different prediction models were compared with traditional pedigree-based models; it was seen an overestimation of genetic parameters for pedigree-based models, even larger when nonadditive effects could not be discerned from additive and residual effects. Prediction accuracies and abilities of the genomic models were sufficient to achieve higher selection efficiencies and responses per year varying between 50-90% by shortening 50% the breeding cycle. For the selection of the top 50 individuals, higher gains were estimated if non-additive effects are incorporated to the models (7 – 117%).
17.	Chaudhary, Rajiv, et al. (författare) Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce 2020 Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10 Tidskriftsartikel (refereegranskat)abstract The Heterobasidion annosum s.l species complex comprises the most damaging forest pathogens to Norway spruce. We revisited previously identified Quantitative Trait Loci (QTLs) related to Heterobasidion-resistance in Norway spruce to identify candidate genes associated with these QTLs. We identified 329 candidate genes associated with the resistance QTLs using a gene-based composite map for Pinaceae. To evaluate the transcriptional responses of these candidate genes to H. parviporum, we inoculated Norway spruce plants and sequenced the transcriptome of the interaction at 3 and 7 days post inoculation. Out of 298 expressed candidate genes 124 were differentially expressed between inoculation and wounding control treatment. Interestingly, PaNAC04 and two of its paralogs in the subgroup III-3 of the NAC family transcription factors were found to be associated with one of the QTLs and was also highly induced in response to H. parviporum. These genes are possibly involved in the regulation of biosynthesis of flavonoid compounds. Furthermore, several of the differentially expressed candidate genes were associated with the phenylpropanoid pathway including a phenylalanine ammonia-lyase, a cinnamoyl-CoA reductase, a caffeoyl-CoA O-methyltransferase and a PgMYB11-like transcription factor gene. Combining transcriptome and genetic linkage analyses can help identifying candidate genes for functional studies and molecular breeding in non-model species.
18.	Chengjiang, Ruan, et al. (författare) Advances in improvement of quality and resistance in a multipurpose crop: sea buckthorn 2013 Ingår i: Critical Reviews in Biotechnology. - : Informa UK Limited. - 0738-8551 .- 1549-7801. ; 33, s. 126-144 Forskningsöversikt (refereegranskat)
19.	Desta, Zeratsion Abera, et al. (författare) Genomic selection: genome-wide prediction in plant improvement 2014 Ingår i: Trends in Plant Science. - : Elsevier BV. - 1360-1385 .- 1878-4372. ; 19, s. 592–601- Forskningsöversikt (refereegranskat)abstract Association analysis is used to measure relations between markers and quantitative trait loci (QTL). Their estimation ignores genes with small effects that trigger underpinning quantitative traits. By contrast, genomewide selection estimates marker effects across the whole genome on the target population based on a prediction model developed in the training population (TP). Whole-genome prediction models estimate all marker effects in all loci and capture small QTL effects. Here, we review several genomic selection (GS) models with respect to both the prediction accuracy and genetic gain from selection. Phenotypic selection or markerassisted breeding protocols can be replaced by selection, based on whole-genome predictions in which phenotyping updates the model to build up the prediction accuracy.
20.	Desta, Zeratsion Abera, et al. (författare) Molecular mapping and identification of quantitative trait loci for domestication traits in the field cress (Lepidium campestre L.) genome 2020 Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. Tidskriftsartikel (refereegranskat)abstract Lepidium campestre (L.) or field cress is a multifaceted oilseed plant, which is not yet domesticated. Moreover, the molecular and genetic mechanisms underlying the domestication traits of field cress remain largely elusive. The overarching goal of this study is to identify quantitative trait loci (QTL) that are fundamental for domestication of field cress. Mapping and dissecting quantitative trait variation may provide important insights into genomic trajectories underlying field cress domestication. We used 7624 single nucleotide polymorphism (SNP) markers for QTL mapping in 428 F-2 interspecific hybrid individuals, while field phenotyping was conducted in F-2:3 segregating families. We applied multiple QTL mapping algorithms to detect and estimate the QTL effects for seven important domestication traits of field cress. Verification of pod shattering across sites revealed that the non-shattering lines declined drastically whereas the shattering lines increased sharply, possibly due to inbreeding followed by selection events. In total, 1461 of the 7624 SNP loci were mapped to eight linkage groups (LGs), spanning 571.9 cM map length. We identified 27 QTL across all LGs of field cress genome, which captured medium to high heritability, implying that genomics-assisted selection could deliver domesticated lines in field cress breeding. The use of high throughput genotyping can accelerate the process of domestication in novel crop species. This is the first QTL mapping analysis in the field cress genome that may lay a foundational framework for positional or functional QTL cloning, introgression as well as genomics-assisted breeding in field cress domestication.
21.	Dida, Mulatu Geleta, et al. (författare) Genetic Diversity within a Global Panel of Durum Wheat (Triticum durum) Landraces and Modern Germplasm Reveals the History of Alleles Exchange 2017 Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 8 Tidskriftsartikel (refereegranskat)abstract Durum wheat is the 10th most important crop in the world, and its use traces back to the origin of agriculture. Unfortunately, in the last century only part of the genetic diversity available for this species has been captured in modern varieties through breeding. Here, the population structure and genetic diversity shared among elites and landraces collected from 32 countries was investigated. A total of 370 entries were genotyped with Axiom 35K array to identify 8,173 segregating single nucleotide polymorphisms (SNPs). Of these, 500 were selected as highly informative with a PIC value above 0.32 and used to test population structure via DAPC, STRUCTURE, and neighbor joining tree. A total of 10 sub-populations could be identified, six constituted by modern germplasm and four by landraces of different geographical origin. Interestingly, genomic comparison among groups indicated that Middle East and Ethiopia had the lowest level of allelic diversity, while breeding programs and landraces collected outside these regions were the richest in rare alleles. Further, phylogenetic analysis among landraces indicated that Ethiopia might represent a second center of origin of durum wheat, rather than a second domestication site as previously believed. Together, the analyses carried here provide a global picture of the available genetic diversity for this crop and shall guide its targeted use by breeders.
22.	Dida, Mulatu Geleta, et al. (författare) Molecular and Genomic Tools Provide Insights on Crop Domestication and Evolution 2016 Ingår i: Advances in Agronomy. - : Elsevier. - 0065-2113 .- 2213-6789. ; 135, s. 181-223 Forskningsöversikt (refereegranskat)abstract Rapid progress in genomic research and the development of genome-wide molecular markers for various crops significantly improved our knowledge on plant domestication and evolution. Molecular markers and other genomic tools have been used to understand the evolutionary changes that converted wild plants into domesticated crops, and the identification of loci behind domestication syndrome traits will have significant importance in the fast-track domestication of new plants. The application of genomics- assisted selection in plant breeding programs has significantly contributed to efficient plant breeding for desirable traits. Genomic tools also facilitated the efficient identification of progenitors of crops as well as centers of domestication. Multiple genomic regions with signature of selection during plant domestication have been found in various crops. Extensive analyses of plant genomes revealed that genes underlying domestication syndrome traits show a significant loss of diversity, for example, up to 95% of genetic diversity in wild relatives has been lost during domestication process in extreme cases. Genomic research revealed repeated occurrence of polyploidization during plant evolution and various interesting events that occurred following polyploidization such as gene loss and silencing. The loss of most replicated genes through time and nonrandom retention of some duplicated genes that serve as signatures of polyploidy are among interesting changes in polyploid plant genomes. Further insights into the advances in our knowledge on plant domestication and evolution made through the use of DNA markers and genomic tools is provided in this paper.
23.	Dubey, Mukesh (författare) Relationship of downy mildew resistance with yield related traits helpful for achieving reliable selection criteria in opium poppy (Papaver somniferum L.) 2015 Ingår i: Indian Journal Of Genetics And Plant Breeding. - : The Indian Society of Genetics and Plant Breeding. - 0019-5200 .- 0975-6906. ; 75, s. 396-399 Tidskriftsartikel (refereegranskat)abstract Present study aims to understand the nature and degree of relationships between different morphometric and yield influencing traits using correlation and path coefficient analysis in medicinally important plant opium poppy. Genotypic and phenotypic correlation coefficients analysis showed significant negative correlation between downy mildew disease severity Index (DSI) and seed and straw yield. Furthermore, path analysis showed direct and positive effect of capsule diameter and number of capsule/plant to straw yield. In contrast, DSI had highest direct and negative contribution to straw yield. These results support effectiveness of selections for high seed and straw yield together with downey mildew-resistance in development of effective selection criteria for crop improvement.
24.	Edvardsson Björnberg, Karin, Docent, 1972-, et al. (författare) The Role of Biotechnology in Sustainable Agriculture : Views and Perceptions Among Key Actors in the Swedish Food Supply Chain 2016 Ingår i: Sustainable Agriculture and Food Supply: Scientific, Economic, and Policy Enhancements. - : Apple Academic Press. - 9781771883849 ; , s. 315-336 Bokkapitel (övrigt vetenskapligt/konstnärligt)
25.	Eriksson, Dennis (författare) A Universally Acceptable View on the Adoption of Improved Plant Breeding Techniques 2017 Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 7 Annan publikation (refereegranskat)
26.	Eriksson, Dennis, et al. (författare) Critical observations on the French Conseil d'Etat ruling on mutagenesis 2020 Ingår i: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 6, s. 1392–1393- Tidskriftsartikel (refereegranskat)
27.	Eriksson, Dennis, et al. (författare) Editorial: Leeway to operate with plant genetic resources 2020 Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 11 Tidskriftsartikel (refereegranskat)abstract Editorial on the Research Topic Leeway to Operate With Plant Genetic Resources Different legal frameworks are applicable to the use of genetic resources (GR). These can broadly be categorized into (1) access and benefit-sharing (ABS), (2) biosafety aspects related to the technologies for improving the genetic material, and (3) intellectual property (IP) systems including plant variety rights (PVR) and patents specific to the plant innovation sector. With scientific and technical progress in research and breeding, as well as expanding internationalization, legal frameworks have become increasingly complex in the past few decades. In this context, the Research Topic “Leeway to operate with plant genetic resources” addresses the latest and most pertinent legalissues related to the use of GR in plant research and breeding.The contributions are summarized here and put into the larger societal and legal context that modern-day plant geneticists are facing.
28.	Eriksson, Dennis (författare) Fact sheets on New Plant Breeding Techniques 2016 Annan publikation (populärvet., debatt m.m.)
29.	Eriksson, Dennis, et al. (författare) Measuring the impact of plant breeding on sub-Saharan African staple crops 2018 Ingår i: Outlook On Agriculture. - : SAGE Publications. - 0030-7270 .- 2043-6866. ; 47, s. 163-180 Forskningsöversikt (refereegranskat)abstract Many countries in sub-Saharan Africa (SSA) are facing huge challenges regarding food insecurity, low agricultural output, and agriculturally incurred environmental degradation. A sustainable and increased crop productivity and diversity is essential to achieve food security in a socially, economically, and environmentally sustainable way. Plant breeding is an important factor contributing to the increased crop productivity and diversity, giving farmers access to genetically improved cultivars that yield more, have better resistance to biotic and abiotic stresses, and meet consumer expectations. To motivate and encourage further investments, it is important to measure the actual impact of breeding. This review considers available research on the impact of breeding through yield gain and of food security, focusing on 10 important staple crops in SSA. The overall impression is that breeding produces a very high return on investment. Such investments remain centerpieces for meeting the challenges in this region. The discussion focuses on the most important future breeding priorities for each crop, the actors involved, and the importance of mechanisms for dissemination and farmer adoption, and concludes with some policy recommendations.
30.	Eriksson, Dennis, et al. (författare) Overview and Breeding Strategies of Table Potato Production in Sweden and the Fennoscandian Region 2016 Ingår i: Potato Research. - : Springer Science and Business Media LLC. - 0014-3065 .- 1871-4528. ; 59, s. 279-294 Tidskriftsartikel (refereegranskat)abstract Recent reductions in the public commitment to potato breeding in Sweden, Norway and Finland call for an evaluation of the current situation regarding the commercial basis for, and structure of, potato breeding in these countries. We here review the extent of cultivation, processing and consumption of table potato in Sweden, as well as provide an overview of the potato breeding tools and programmes in the three countries. We then discuss various strategies to provide long-term stability and increase the impact of public potato breeding, based on the similar overall conditions for potato cultivation across the Fennoscandian region. The conclusions are twofold; first, an increased long-term funding of the public potato breeding programmes is necessary to maintain a minimum level of material, and second, a coordination of the breeding activities in the Fennoscandian region would be of great benefit to all involved stakeholders and allow an enhancement of the current national breeding programmes. In addition, we propose a minimum first field year population size for potato breeding.
31.	Eriksson, Dennis (författare) Regulatory hurdles for genome editing: process- vs. product-based approaches in different regulatory contexts 2016 Ingår i: Plant Cell Reports. - : Springer Science and Business Media LLC. - 0721-7714 .- 1432-203X. ; 35, s. 1493-1506 Tidskriftsartikel (refereegranskat)abstract Novel plant genome editing techniques call for an updated legislation regulating the use of plants produced by genetic engineering or genome editing, especially in the European Union. Established more than 25 years ago and based on a clear distinction between transgenic and conventionally bred plants, the current EU Directives fail to accommodate the new continuum between genetic engineering and conventional breeding. Despite the fact that the Directive 2001/18/EC contains both process- and product-related terms, it is commonly interpreted as a strictly process-based legislation. In view of several new emerging techniques which are closer to the conventional breeding than common genetic engineering, we argue that it should be actually interpreted more in relation to the resulting product. A legal guidance on how to define plants produced by exploring novel genome editing techniques in relation to the decade-old legislation is urgently needed, as private companies and public researchers are waiting impatiently with products and projects in the pipeline. We here outline the process in the EU to develop a legislation that properly matches the scientific progress. As the process is facing several hurdles, we also compare with existing frameworks in other countries and discuss ideas for an alternative regulatory system.
32.	Fagerström, Torbjörn, et al. (författare) Plant Biotechnology For a Bio-Based Economy 2014 Rapport (övrigt vetenskapligt/konstnärligt)
33.	Gebeyehu Demissie, Adane, et al. (författare) RNA-Seq Provides Novel Genomic Resources for Noug (Guizotia abyssinica) and Reveals Microsatellite Frequency and Distribution in Its Transcriptome 2022 Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13 Tidskriftsartikel (refereegranskat)abstract Genomic resources and tools are essential for improving crops and conserving their genetic resources. Guizotia abyssinica (noug), an outcrossing edible oilseed crop, has highly limited genomic resources. Hence, RNA-Seq based transcriptome sequencing of 30 noug genotypes was performed to generate novel genomic resources and assess their usefulness. The genotypes include self-compatible and self-incompatible types, which differ in maturity time, photoperiod sensitivity, or oil content and quality. RNA-Seq was performed on Illumina HiSeq 2500 platform, and the transcript was reconstructed de novo, resulting in 409,309 unigenes. The unigenes were characterized for simple sequence repeats (SSRs), and served as a reference for single nucleotide polymorphism (SNP) calling. In total, 40,776 SSRs were identified in 35,639 of the 409,309 unigenes. Of these, mono, di, tri, tetra, penta and hexanucleotide repeats accounted for 55.4, 20.8, 21.1, 2.3, 0.2, and 0.2%, respectively. The average G+C content of the unigenes and their SSRs were 40 and 22.1%, respectively. The vast majority of mononucleotide repeat SSRs (97%) were of the A/T type. AG/CT and CCA/TGG were the most frequent di and trinucleotide repeat SSRs. A different number of single nucleotide polymorphism (SNP) loci were discovered in each genotype, of which 1,687 were common to all 30 genotypes and 5,531 to 28 of them. The mean observed heterozygosity of the 5,531 SNPs was 0.22; 19.4% of them had polymorphism information content above 0.30 while 17.2% deviated significantly from Hardy-Weinberg equilibrium (P < 0.05). In both cluster and principal coordinate analyses, the genotypes were grouped into four major clusters. In terms of population structure, the genotypes are best represented by three genetic populations, with significant admixture within each. Genetic similarity between self-compatible genotypes was higher, due to the narrow genetic basis, than that between self-incompatible genotypes. The genotypes that shared desirable characteristics, such as early maturity, and high oil content were found to be genetically diverse, and hence superior cultivars with multiple desirable traits can be developed through crossbreeding. The genomic resources developed in this study are vital for advancing research in noug, such as genetic linkage mapping and genome-wide association studies, which could lead to genomic-led breeding.
34.	Ghasemkhani, Marjan (författare) Genetic basis for resistance against fruit tree canker in apple 2012 Rapport (övrigt vetenskapligt/konstnärligt)abstract Neonectria ditissima (formerly Neonectria galligena, anamorph Cylindrocarpon heteronema) is the causal agent of fruit tree canker which is regarded as a serious economic problem in horticulture. This fungus causes notable damage to apple trees and it is very important in some regions, especially North western Europe, where it can result in death of spur shoots and branches. Although it occurs in a wide range of temperatures, it is associated with wet weather and climate has an important effect on the geographic distribution. The fungus produces conidia and ascospores, both of which are dispersed and cause infection during prolonged periods of rainy weather. Also, spores produced on the infected wood can act as an infection source in the orchards. The fungus can therefore be introduced into new orchards with infected planting material from other orchards or tree nurseries. Chemical and mechanical control like spraying of fungicides, covering wounds with paint, and cutting out infected branches, do not prevent the occurrence of epidemics. Breeding cultivars with a high level of resistance towards canker would be of great help towards the avoidance of this disease. Apple cultivars show variable levels of partial resistance to the fungus, whereas complete resistance has not yet been reported and no major genes have been identified. Therefore, apple genotypes with comparatively high levels of genetically determined partial resistance should be identified for use in apple breeding.
35.	Gustavsson, Larisa, et al. (författare) Resistance to Neonectria ditissima in apple : insights from metabolomics and lipidomics analyses 2023 Ingår i: Xxxi international horticultural congress (ihc2022). - : International Society for Horticultural Science. - 9789462613614 ; , s. 329-335, s. 329-336 Konferensbidrag (refereegranskat)abstract European canker, caused by the necrotrophic fungus Neonectria ditissima, is the most serious disease in apple production in Sweden. The disease is favored by a relatively cool and rainy climate. The canker damages have a significant economic impact due to reduced bearing surface and increased orchard management costs. The possibilities for chemical and biological control are very limited. Therefore, directed breeding for new resistant cultivars is urgently needed. Knowledge of inheritance of canker resistance and understanding of molecular mechanisms involved in resistant and susceptible responses to fungal attacks would facilitate breeding. In this study, we evaluated the tempo-spatial differences in plant-pathogen interactions in a set of partially resistant and susceptible cultivars by conducting metabolomic and lipidomic analyses. The major trends in metabolomics and lipidomic profiles were common among cultivars, irrespective of the degree of susceptibility. Several metabolites and lipids varied with time point and cultivar under N. ditissima infection. Putative key metabolites such as suberic acid and jasmonic acid were upregulated in all cultivars upon infection. Additionally, several lipids exhibited changes 30 to 45 days post-inoculation. Thus, the approach used seems to have resulted in a rich data set to be further analyzed in light of ongoing QTL-mapping efforts.
36.	Hammenhag, Cecilia, et al. (författare) Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars 2021 Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 12 Tidskriftsartikel (refereegranskat)abstract Finger millet (Eleusine coracana (L.) Geartn.) is a self-pollinating amphidiploid crop cultivated with minimal input for food and feed, as well as a source of income for small-scale farmers. To efficiently assess its genetic diversity for conservation and use in breeding programs, polymorphic DNA markers that represent its complex tetraploid genome have to be developed and used. In this study, 13 new expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on publicly available finger millet ESTs. Using 10 polymorphic SSR markers (3 genomic and 7 novel EST-derived), the genetic diversity of 55 landrace accessions and 5 cultivars of finger millet representing its major growing areas in Ethiopia was assessed. In total, 26 alleles were detected across the 10 loci, and the average observed number of alleles per locus was 5.6. The polymorphic information content (PIC) of the loci ranged from 0.045 (Elco-48) to 0.71 (UGEP-66). The level of genetic diversity did not differ much between the accessions with the mean gene diversity estimates ranging only from 0.44 (accession 216054) to 0.68 (accession 237443). Similarly, a narrow range of variation was recorded at the level of regional states ranging from 0.54 (Oromia) to 0.59 (Amhara and Tigray). Interestingly, the average gene diversity of the landrace accessions (0.57) was similar to that of the cultivars (0.58). The analysis of molecular variance (AMOVA) revealed significant genetic variation both within and among accessions. The variation among the accessions accounted for 18.8% of the total variation (FST = 0.19; P < 0.001). Similarly, significant genetic variation was obtained among the geographic regions, accounting for 6.9% of the total variation (P < 0.001). The results of the cluster, principal coordinate, and population structure analyses suggest a poor correlation between the genetic makeups of finger millet landrace populations and their geographic regions of origin, which in turn suggests strong gene flow between populations within and across geographic regions. This study contributed novel EST-SSR markers for their various applications, and those that were monomorphic should be tested in more diverse finger millet genetic resources.
37.	Hammenhag, Cecilia, et al. (författare) QTL mapping for domestication-related characteristics in field cress (Lepidium campestre)—a novel oil crop for the Subarctic region 2020 Ingår i: Genes. - : MDPI AG. - 2073-4425. ; 11 Tidskriftsartikel (refereegranskat)abstract Domestication of a new crop requires identification and improvement of desirable characteristics Field cress (Lepidium campestre) is being domesticated as a new oilseed crop, particularly for northern temperate regions.. In the present study, an F-2 mapping population and its F-3 progenies were used to identify quantitative trait loci (QTLs) for plant height (PH), number of stems per plant (NS), stem growth orientation (SO), flowering habit (FH), earliness (ER), seed yield per plant (SY), pod shattering resistance (SHR), and perenniality (PE). A highly significant correlation (p < 0.001) was observed between several pairs of characteristics, including SY and ER (negative) or ER and PE (positive). The inclusive composite interval mapping approach was used for QTL mapping using 2330 single nucleotide polymorphism (SNP) markers mapped across the eight field cress linkage groups. Nine QTLs were identified with NS, PH, SO, and PE having 3, 3, 2, and 1 QTLs, explaining 21.3%, 29.5%, 3.8%, and 7.2% of the phenotypic variation, respectively. Candidate genes behind three of the QTLs and favorable marker alleles for different classes of each characteristic were identified. Following their validation through further study, the identified QTLs and associated favorable marker alleles can be used in marker-aided breeding to speed up the domestication of field cress.
38.	Hegay, Sergay (författare) Diversity of beans grown in Kyrgyzstan and marker-aided breeding for resistance to Bean common mosaic virus and anthracnose 2013 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Common bean (Phaseolus vulgaris L.) is an important export crop in Kyrgyzstan since the end of the 20th century. Kyrgyzstan produces about 70,000 t of common beans per year, which provides jobs to 76% of the population in the Talas region. Information about genetic diversity of common beans helps to select appropriate genetic material to be used for breeding programs. Accessions originating from both Mesoamerican and Andean gene pools, including the main Kyrgyz common bean market types were analyzed using simple sequence repeats (SSR) and qualitative morphological traits. The similarity matrices generated from the molecular and morphological data were well correlated (r = 0.49**). The cluster analysis of both data sets grouped the accessions according to their gene pools of origin, where Mesoamerican accessions were more diverse than Andean accessions. Both SSR and qualitative morphological markers were suitable for assigning cultivars to their gene pools of origin. Furthermore, information about traits of interest for Kyrgyz farmers has been gained. We found that Bean common mosaic virus strain NL6 and anthracnose affect this crop and reduce its grain yield significantly in Kyrgyzstan. The susceptible Kyrgyz cultivars Ryabaya, Kytayanka and Lopatka were included as recurrent parents in a backcrossing breeding scheme for introducing host plant resistance to these diseases from donor cultivars. After the 4th backcross, seeds (color, shape, size) and pods (shape) were similar to the respective recurrent parent. The sequence characterized amplified region (SCAR) markers SW13, SBD5 and SCAreoli were used successfully in marker-aided backcrossing for pyramiding the I, bc-12 and Co-2 genes, which provide host plant resistance to BCMV and anthracnose, respectively. Inoculation tests with anthracnose races delta and gamma, virus strain NL3, and DNA markers confirmed the presence of resistance genes in the offspring.
39.	Hennigs, Lars (författare) FLOWERING LOCUS T Triggers Early and Fertile Flowering in Glasshouse Cassava (Manihot esculenta Crantz) 2017 Ingår i: Plants. - : MDPI AG. - 2223-7747. ; 6 Tidskriftsartikel (refereegranskat)abstract Accelerated breeding of plant species has the potential to help challenge environmental and biochemical cues to support global crop security. We demonstrate the over-expression of Arabidopsis FLOWERING LOCUS T in Agrobacterium-mediated transformed cassava (Manihot esculenta Crantz; cultivar 60444) to trigger early flowering in glasshouse-grown plants. An event seldom seen in a glasshouse environment, precocious flowering and mature inflorescence were obtained within 4–5 months from planting of stem cuttings. Manual pollination using pistillate and staminate flowers from clonal propagants gave rise to viable seeds that germinated into morphologically typical progeny. This strategy comes at a time when accelerated crop breeding is of increasing importance to complement progressive genome editing techniques.
40.	Hörnblad, Emma (författare) Synthesis of glucuronoxylan in higher and lower plants : is there conservation of the enzymatic machinery? 2012 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract The hemicellulose glucuronoxylan (GX) is the second most abundant polysaccharide after cellulose in the secondary cell walls of angiosperms and contributes significantly to the properties of wood as raw materials. Despite this, very little is known about the biosynthesis of hemicellulose. The thesis is based on studies performed in Physcomitrella patens, Arabidopsis thaliana, and Populus plants with the aim to increase the understanding of glucuronoxylan synthesis, and with main focus on the role of the IRX10 gene family. A number of genes have proven to be involved in GX biosynthesis in Arabidopsis, namely IRREGULAR XYLEM (IRX) 9, IRX14, IRX8, FRAGILE FIBER (FRA) 8 and PARVUS. This thesis presents two new genes, IRX10 and its close homolog IRX10- LIKE (L), which can now be added to the group of presumed GX biosynthesis genes. In addition, identification and characterisation of three homologs (IRX9-L, IRX14-L and F8H) of previously identified GX synthesis genes is described. Complementation experiments and morphological studies confirmed redundancy between the IRX9 and IRX9-L, IRX14 and IRX14-L, and the FRA8 and F8H pairs of genes in Arabidopsis. A bioinformatics based approach has led to the identification of four putative homologs in Populus trichocarpa (PtGT47A-1, PtGT47A-2, PtGT47D-1, and PtGT47D-4) of AtIRX10, and one putative homolog from Physcomitrella (PpGT47D). Experiments further confirmed functional conservation between the Arabidopsis (IRX10) and Populus GT47A proteins, and partial functional conservation between the Populus GT47D, the Physcomitrella GT47D and Arabidopsis IRX10 proteins. The work supports the existence of an Arabidopsis GX backbone biosynthesis complex in which AtIRX10 and AtIRX10-L form an essential component together with AtIRX9 and AtIRX14. It also suggests that parts of the GX biosynthesis machinery are conserved across embryophytes. Finally, work presented in this thesis indicates that the IRX10 gene family has gone through a subfunctionalisation event during the evolution.
41.	Ivarson, Emelie (författare) Development of Lepidium campestre into a new oil and catch crop 2016 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract A growing world population and dwindling fossil oil reserves demand an increase in the world plant oil production. The possibility to increase the area of cultivated land is limited due to the shortage of arable land. Also, the possibility for increasing the oil content in the limited number of cultivated oil crops is restricted. New, high-yielding oil crops, which can be grown in areas where no other oil crops can grow and have less environmental impact, need to be developed. It is preferable that such new oil crops would allow us to tailor-make the oil composition in planta for food, fuel or industrial applications. In Sweden, the main oil crop cultivated is winter rapeseed, which, due to weak winter hardiness, only can be grown in southern Sweden. Developing a new winter-hardy oilseed crop would extend the plant oil production in Sweden and other cold climate regions. Lepidium campestre is a wild Brassica species. It is very winter hardy, high-yielding, has an upright stature and synchronous flowering. Moreover, it is biennial, and thus being suitable as a catch crop. However, it needs to be domesticated first so that it possesses all important agronomic traits necessary for being a successful agricultural crop. The aim of this thesis was to improve some properties of L. campestre by genetic engineering with focus on: the seed oil content, pod shatter, seed oil composition and wax ester production in the seed oil. In order to enable genetic engineering of this wild species, a well-functioning regeneration and transformation protocol was first developed, which has greatly facilitated the subsequent genetic improvements of the target traits of the species. Through RNAi-down-regulation of the FAD2 and FAE1 genes, transgenic lines with oxidative stable oil high in oleic acid were generated, indicating the potential of the species for being used for food oil purposes. Moreover, transgenic lines with increased seed oil content were developed by expressing either the AtWRI1 or AtHb2 or BvHb2 gene. Transgenic lines with pod shatter resistance were produced by RNAi down-regulation of the IND gene. Wax esters were produced in this species by expression of the jojoba wax synthesis genes, showing the potential of the species as a new platform for industrial oil production. These transgenic lines are valuable materials for further breeding of this species.
42.	Ivarson, Emelie, et al. (författare) Effects of overexpression of WRI1 and hemoglobin genes on the seed oil content of Lepidium campestre 2017 Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 7 Tidskriftsartikel (refereegranskat)abstract The wild species field cress (Lepidium campestre), belonging to the Brassicaceae family, has potential to be developed into a novel oilseed- and catch crop, however, the species needs to be further improved regarding some important agronomic traits. One of them is its low oil content which needs to be increased. As far as we know there is no study aiming at increasing the oil content that has been reported in this species. In order to investigate the possibility to increase the seed oil content in field cress, we have tried to introduce the Arabidopsis WRINKLED1 (AtWRI1) or hemoglobin (Hb) genes from either Arabidopsis thaliana (AtHb2) or Beta vulgaris (BvHb2) into field cress with the seed specific expression. The hypothesis was that the oil content would be increased by overexpressing these target genes. The results showed that the oil content was indeed increased by up to 29.9, 20.2, and 25.9% in the transgenic lines expressing AtWRI1, AtHb2, and BvHb2, respectively. The seed oil composition of the transgenic lines did not significantly deviate from the seed oil composition of the wild type plants. Our results indicate that genetic modification can be used in this wild species for its fast domestication into a future economically viable oilseed and catch crop.
43.	Jin, Yunkai, et al. (författare) New Energy Crops for Biofuel Production 2015 Ingår i: Handbook of clean energy systems. - Chichester, UK : John Wiley & Sons, Ltd. - 9781118388587 ; , s. 49-62 Bokkapitel (refereegranskat)
44.	Karlsson, Milla, et al. (författare) Möjliga tillämpningar av nya genomiska tekniker inom integrerat växtskydd 2023 Rapport (övrigt vetenskapligt/konstnärligt)abstract Det pågår en omställning av jord- och trädgårdsbruket, både med hänsyn till hållbar produktion och pågående klimatförändringar. Som en del av EUs arbete att utveckla lantbruket mot en mer hållbar produktion har kommissionen lagt fram ett förslag på minskning av växtskyddsmedel om minst 50 %, totalt sett inom EU, senast 2030. För Sveriges del innebär förslaget, enligt preliminära beräkningar, att vi behöver minska mängden växtskyddsmedel med 35-36 %. För att ersätta funktionen av denna mängd växtskyddsmedel behövs ett integrerat tillvägagångssätt som kräver tillgång till andra effektiva metoder för bekämpning av skadegörare på odlade växter.Under det senaste decenniet har nya genomiska tekniker inom växtförädlingen utvecklats, vilka möjliggör riktade förändringar i många grödors genom. Teknikerna innebär antingen att man introducerar enstaka förändringar i DNA-sekvensen (s.k. genomredigering), eller att man sätter in en längre DNA-sekvens från samma art eller en korsningsbar art i en gröda (s.k. cisgenes). Dessutom har kunskapen om växters försvarssystem framskridit avsevärt. Med den ökade kunskapen och de nya teknikerna ökar möjligheten att kombinera gener och öka variationen av de gener som gör grödorna resistenta mot olika växtsjukdomar. På så sätt kan förädlingen av sjukdomsresistenta sorter ske med betydligt bättre precision och på kortare tid än vad traditionella förädlingstekniker tillåter. Tidsaspekten kan ses som extra viktig i resistenssammanhang eftersom skadegörarpopulationerna ändras kontinuerligt. Potentialen att kombinera flera olika resistensmekanismer för att uppnå mer uthållig resistens samt möjligheten att lösa ett eller flera växtskyddsproblem i samma sort bör också noteras.Enligt nuvarande EU-lagstiftning regleras dock genomredigerade och cisgena grödor på samma sätt som traditionellt genetiskt modifierade organismer (GMO), en lagstiftning som i praktiken omöjliggör kommersiell odling inom EU. Detta trots att resultatet av de moderna teknikerna kan efterlikna vad som kan ske spontant i naturen (mutationer) eller via traditionella oreglerade förädlingsmetoder (t.ex. mutations-, eller korsningsförädling). I lagstiftningen tas det ej i beaktande att sjukdomsresistenta grödor kan bidra till en minskad användning av växtskyddsmedel.Idag är potatisodling ofta förknippad med en användning av stora mängder växtskyddsmedel mot potatisbladmögel. Samtidigt är det möjligt att göra potatissorterna helt resistenta mot potatisbladmögel med hjälp av cisgenes och ge dem en ökad motståndskraft med hjälp av genomredigering. Om det vore möjligt att odla potatis som förädlats med nya genomiska tekniker inom EU idag, visar denna rapport att det skulle vara möjligt att kraftigt minska användningen av växtskyddsmedel i potatisodlingen. Det skulle innebära en reducering av mängden växtskyddsmedel som används inom det svenska lantbruket och skulle även innebära besparingar runt 91 miljoner SEK per år för odlarna.Vete och annan spannmål är de grödor där flest totala hektardoser av fungicider appliceras, till en årlig kostnad av två miljarder SEK. För dessa grödor finns inget lika tydligt exempel på enskilda sjukdomar som så kraftigt kan minska fungicidanvändningen. Vi ser dock en tydlig framtida potential att minska antalet bekämpningar och därmed kostnaden för lantbruket med hjälp av nya genomiska tekniker inom sädesslagen.Möjligheten att öka växters egen resistens för att minska användningen av växtskyddsmedel finns redan idag även i flera andra grödor, och möjligheterna förväntas fortsatt växa i takt med att teknikutveckling och forskning fortgår. En förändrad lagstiftning runt nya genomiska tekniker skulle även öppna för applikationer inom områden där det idag inte finns någon effektiv metod att bekämpa växtskadegörare. Exempel på sådana skadegörare är många virussjukdomar och skador som orsakas av nematoder. Därför kan skördestabiliteten och konkurrenskraften förväntas öka i grödor där det idag finns skadegörare där effektiva bekämpningsmetoder saknas.Sammanfattningsvis ser vi nya genomiska tekniker för att förädla resistenta grödor som en viktig del i arbetet mot ett hållbart jordbruk och för att uppnå EU-kommissionens mål om att reducera användningen av växtskyddsmedel inom jord- och trädgårdsbruket.
45.	Kianersi, Farzad, et al. (författare) Biosynthesis of rutin changes in Capparis spinosa due to altered expression of its pathway genes under elicitors' supplementation 2020 Ingår i: Plant Cell Tissue and Organ Culture. - : Springer Nature. - 0167-6857 .- 1573-5044. ; 141:3, s. 619-631 Tidskriftsartikel (refereegranskat)abstract Caper plant is (Capparis spinosa L.) a good source of rutin which plays a key role in the human diet. In this study, the effect of different concentrations of salicylic acid (SA) and methyl jasmonate (MeJA) on the weight of anther-derived calli and their rutin contents were assessed in caper plants. Also, we investigated the rutin content and expression pattern of some rutin related genes in leaves of caper plants at vegetative and fresh fruiting growth stages under SA and MeJA treatments. In the first experiment, the highest rutin contents were observed in anther-derived calli treated with 10 mu M MeJA and 100 mg L-1 SA after 2 weeks from initial treatments, which were 2.44 and 2.22-fold higher than control. Also, the treatment of caper plants with150 mu M MeJA and 100 mg L-1 SA resulted in a higher increase in the rutin content of leaves at the fresh fruiting stage (61.46 and 9.99 mg g(-1) DW, respectively), in the second experiment. Among the studied genes, the FLS gene showed the highest expression in the leaves of the MeJA- and SA-treated plants at vegetative growth stage, while in the fresh fruiting stage the highest expression was related to the RT gene. Use of 150 mu M MeJA and 100 mg L-1 SA enhanced the expression levels of the RT gene up to 7.36 and 2.89 times of the control, respectively. These results suggest that rutin content and the expression patterns of rutin biosynthesis genes in caper can be significantly enhanced by the SA and MeJA treatments in a growth stage-dependent manner. Key message Methyl jasmonate and salicylic acid treatments enhance the rutin contents of Capparis spinosa in vitro and in vivo and up-regulate the rutin biosynthetic related genes at two different growth stages.
46.	Lehrman, Anna, et al. (författare) Framtidens mat - om husdjursavel och växtförädling 2014 Bok (övrigt vetenskapligt/konstnärligt)abstract Du har kanske inte funderat över varför tomater ser ut som de gör, varför våra husdjur är så lugna och vänliga, eller hur det är möjligt att köpa en vattenmelon utan kärnor. Trots att växtförädling och djuravel har format det mesta vi äter, är det få människor som är medvetna om vilka vetenskapliga upptäckter och vilket omfattande arbete som ligger bakom maten vi lägger på våra tallrikar. Med den här boken vill vi ge en översikt över domesticeringens och förädlingens bakgrund, från jordbrukets början för mer än 10 000 år sedan till dagens molekylära arbete. Vi beskriver grunderna för genernas strukturer och funktioner, varför och hur olika avels- och förädlingsmetoder används och ger en inblick i lagstiftningen kring användning av genteknik i Sverige och EU. Vi ger också en överblick över olika produkter som tagits fram genom genetisk modifiering (GM) och en sammanfattning av de ekonomiska konsekvenserna av GM-grödor. Vidare diskuterar vi etiska frågor som rör avel och förädling i allmänhet och genetisk modifiering i synnerhet.
47.	Leonova, Svetlana (författare) Lipids in seeds of oat (Avena spp.), a potential oil crop : content, quality, metabolism, and possibilities for improvement 2013 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract New oil crops with high yield and oil content are urgently needed. Oat is the only cereal that accumulates substantial amount of lipids in the endosperm. This gives it potential as an oil crop, which could address both nutritional and environmental concerns of modern society. To develop oat with increased oil content, thorough investigations on its lipid metabolism and tools for genetic manipulations are needed. Analyses of lipids in seeds of wild and cultivated oat species revealed variation in wild oat accessions in both oil content and quality. This variation should allow for development of new oat varieties for diverse applications. However, to develop oat as an oil crop, a level of 20% of the seed dry weight as oil is required and the range of oil content in the studied accessions was 4-10%. Another feature which showed almost no deviation was the amount of omega 3 fatty acid, -linolenic acid (0.6-2.1%). To develop oat varieties with ultra-high seed oil and increased content of omega 3 fatty acids, a biotechnological approach is preferred to conventional breeding methods. Lipids in oat endosperm have been reported to exist, not enclosed in oil bodies, but as non-structured oil smear. In my study, I also observed oil smears, a phenomenon probably correlated with the reduced amount of oil body associated proteins in the endosperm, as revealed by microscopic and staining methods. This was supported experimentally by SDS-PAGE separation of oil-body proteins and immunoblotting and immunolocalization with antibodies against a 16 kD oil body protein. Biochemical studies on lipid mobilization during oat seed germination demonstrated efficient utilization of oil reserves from the starchy endosperm; these results were corroborated by microscopy. An oat cultivar which is capable of accumulating high amounts of oil in the endosperm was shown to be also efficient in utilizing these reserves upon germination. Agrobacterium-mediated transformation is one of the methods for modification of oat oil content and/or its quality. The results of the analyses aimed at development of an Agrobacterium-mediated oat transformation protocol are presented in this thesis.
48.	Mehrabi, Sara, 1982-, et al. (författare) The constitutive expression and induction of three β-1,3-glucanases by bird cherry-oat aphid in relation to aphid resistance in 15 barley breeding lines 2016 Ingår i: Arthropod-Plant Interactions. - : Springer Science and Business Media LLC. - 1872-8855 .- 1872-8847. ; 10:2, s. 101-111 Tidskriftsartikel (refereegranskat)abstract In this study, 15 closely related barley genotypes were analyzed for the abundance of three β-1,3-glucanase transcripts immediately before and during infestation by the bird cherry-oat aphid (Rhopalosiphum padi L.). The barley lines are doubled haploid lines in backcross (BC) generations BC1 and BC2 from a cross between cultivar Lina and a wild barley accession. Previously, they have been characterized as susceptible (S) or resistant (R) to R. padi based on their ability to support nymphal growth. Here we also tested whether resistance was manifested as reduced aphid settling on the plants. Indeed, aphid numbers were lower on R than on S lines in all cases where there were significant differences between R and S lines. The choice of β-1,3-glucanase sequences is based on earlier results comparing two S and two R genotypes, suggesting that at least two of the three studied sequences are susceptibility factors. The comparisons of transcript abundance in plants with aphids showed for two of the β-1,3-glucanase sequences that there were several cases where an S genotype had significantly higher abundance than an R genotype, and in no case did an R line have significantly higher abundance than an S line. Thus, there was some support for the idea that β-1,3-glucanase sequences are susceptibility factors in the interaction between barley and R. padi.
49.	Mulugeta, Behailu, et al. (författare) Marker-trait association analyses revealed major novel QTLs for grain yield and related traits in durum wheat 2023 Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13 Tidskriftsartikel (refereegranskat)abstract The growing global demand for wheat for food is rising due to the influence of population growth and climate change. The dissection of complex traits by employing a genome-wide association study (GWAS) allows the identification of DNA markers associated with complex traits to improve the productivity of crops. We used GWAS with 10,045 single nucleotide polymorphism (SNP) markers to search for genomic regions associated with grain yield and related traits based on diverse panels of Ethiopian durum wheat. In Ethiopia, multi-environment trials of the genotypes were carried out at five locations. The genotyping was conducted using the 25k Illumina Wheat SNP array to explore population structure, linkage disequilibrium (LD), and marker-trait associations (MTAs). For GWAS, the multi-locus Fixed and Random Model Circulating Probability Unification (FarmCPU) model was applied. Broad-sense heritability estimates were high, ranging from 0.63 (for grain yield) to 0.97 (for thousand-kernel weight). The population structure based on principal component analysis, and model-based cluster analysis revealed two genetically distinct clusters with limited admixtures. The LD among SNPs declined within the range of 2.02-10.04 Mbp with an average of 4.28 Mbp. The GWAS scan based on the mean performance of the genotypes across the environments identified 44 significant MTAs across the chromosomes. Twenty-six of these MTAs are novel, whereas the remaining 18 were previously reported and confirmed in this study. We also identified candidate genes for the novel loci potentially regulating the traits. Hence, this study highlights the significance of the Ethiopian durum wheat gene pool for improving durum wheat globally. Furthermore, a breeding strategy focusing on accumulating favorable alleles at these loci could improve durum wheat production in the East African highlands and elsewhere.
50.	Nemesio Gorriz, Miguel (författare) Molecular responses against Heterobasidion annosum s.l. in Picea abies 2015 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Norway spruce [Picea abies (L.) Karst.] is a main tree species in European forests and is important both ecologically and economically. The root rot fungus Heterobasidion annosum sensu lato (s.l.) is the main P. abies pathogen. Including resistance in breeding programs would help mitigating the impact of the pathogen but knowledge regarding defense mechanisms in P. abies needs a better understanding. The work within this thesis intended to expand the existing knowledge on P. abies resistance mechanisms focusing on hormone signaling, flavonoid biosynthesis and its transcriptional regulation. I found that jasmonic acid is the major hormone controlling defense signaling pathways in P. abies. Furthermore, we validated a candidate gene, PaLAR3, as a resistance marker for H. annosum s.l. in P. abies. PaLAR3 encodes an enzyme responsible for the synthesis of (+) catechin, which showed a fungistatic effect on H. parviporum. Analysis of genetic diversity revealed two allelic lineages of PaLAR3 that showed significant differences in fungal resistance and (+) catechin content that were explained by dissimilarities in inducibility. We studied the role of PaNAC03, a transcription factor that is associated with H. annosum s.l. infection. PaNAC03 not only showed repression of multiple genes including PaLAR3, but bound only to the promoter of one of the PaLAR3 allelic lineages explaining at least partly the differences in allelic expression that were observed. Finally, we identified a full repertoire of members of a MYB/bHLH/WDR transcription factor complex in Norway spruce, which showed differences in protein interactions and expression patterns, and also in ability to control the expression of genes in the flavonoid biosynthetic pathway including PaLAR3.

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